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Montenont E, Bhatlekar S, Jacob S, Kosaka Y, Manne BK, Lee O, Parra-Izquierdo I, Tugolukova E, Tolley ND, Rondina MT, Bray PF, Rowley JW. CRISPR-edited megakaryocytes for rapid screening of platelet gene functions. Blood Adv 2021; 5:2362-2374. [PMID: 33944898 PMCID: PMC8114553 DOI: 10.1182/bloodadvances.2020004112] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/09/2021] [Indexed: 01/07/2023] Open
Abstract
Human anucleate platelets cannot be directly modified using traditional genetic approaches. Instead, studies of platelet gene function depend on alternative models. Megakaryocytes (the nucleated precursor to platelets) are the nearest cell to platelets in origin, structure, and function. However, achieving consistent genetic modifications in primary megakaryocytes has been challenging, and the functional effects of induced gene deletions on human megakaryocytes for even well-characterized platelet genes (eg, ITGA2B) are unknown. Here we present a rapid and systematic approach to screen genes for platelet functions in CD34+ cell-derived megakaryocytes called CRIMSON (CRISPR-edited megakaryocytes for rapid screening of platelet gene functions). By using CRISPR/Cas9, we achieved efficient nonviral gene editing of a panel of platelet genes in megakaryocytes without compromising megakaryopoiesis. Gene editing induced loss of protein in up to 95% of cells for platelet function genes GP6, RASGRP2, and ITGA2B; for the immune receptor component B2M; and for COMMD7, which was previously associated with cardiovascular disease and platelet function. Gene deletions affected several select responses to platelet agonists in megakaryocytes in a manner largely consistent with those expected for platelets. Deletion of B2M did not significantly affect platelet-like responses, whereas deletion of ITGA2B abolished agonist-induced integrin activation and spreading on fibrinogen without affecting the translocation of P-selectin. Deletion of GP6 abrogated responses to collagen receptor agonists but not thrombin. Deletion of RASGRP2 impaired functional responses to adenosine 5'-diphosphate (ADP), thrombin, and collagen receptor agonists. Deletion of COMMD7 significantly impaired multiple responses to platelet agonists. Together, our data recommend CRIMSON for rapid evaluation of platelet gene phenotype associations.
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Affiliation(s)
- Emilie Montenont
- Molecular Medicine Program, The University of Utah, Salt Lake City, UT
| | - Seema Bhatlekar
- Molecular Medicine Program, The University of Utah, Salt Lake City, UT
| | - Shancy Jacob
- Molecular Medicine Program, The University of Utah, Salt Lake City, UT
| | - Yasuhiro Kosaka
- Molecular Medicine Program, The University of Utah, Salt Lake City, UT
| | - Bhanu K Manne
- Molecular Medicine Program, The University of Utah, Salt Lake City, UT
| | - Olivia Lee
- Molecular Medicine Program, The University of Utah, Salt Lake City, UT
| | | | - Emilia Tugolukova
- Molecular Medicine Program, The University of Utah, Salt Lake City, UT
| | - Neal D Tolley
- Molecular Medicine Program, The University of Utah, Salt Lake City, UT
| | - Matthew T Rondina
- Molecular Medicine Program, The University of Utah, Salt Lake City, UT
- Department of Internal Medicine
- George E. Wahlen Department of Veterans Affairs Medical Center
- Department of Internal Medicine and Geriatric Research and Education Clinical Center, and
- Department of Pathology, The University of Utah, Salt Lake City, UT
| | - Paul F Bray
- Molecular Medicine Program, The University of Utah, Salt Lake City, UT
- Department of Internal Medicine
| | - Jesse W Rowley
- Molecular Medicine Program, The University of Utah, Salt Lake City, UT
- Department of Internal Medicine
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Polewko-Klim A, Lesiński W, Golińska AK, Mnich K, Siwek M, Rudnicki WR. Sensitivity analysis based on the random forest machine learning algorithm identifies candidate genes for regulation of innate and adaptive immune response of chicken. Poult Sci 2020; 99:6341-6354. [PMID: 33248550 PMCID: PMC7704721 DOI: 10.1016/j.psj.2020.08.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 07/14/2020] [Accepted: 08/11/2020] [Indexed: 11/25/2022] Open
Abstract
Two categories of immune responses—innate and adaptive immunity—have both polygenic backgrounds and a significant environmental component. The goal of the reported study was to define candidate genes and mutations for the immune traits of interest in chickens using machine learning–based sensitivity analysis for single-nucleotide polymorphisms (SNPs) located in candidate genes defined in quantitative trait loci regions. Here the adaptive immunity is represented by the specific antibody response toward keyhole limpet hemocyanin (KLH), whereas the innate immunity was represented by natural antibodies toward lipopolysaccharide (LPS) and lipoteichoic acid (LTA). The analysis consisted of 3 basic steps: an identification of candidate SNPs via feature selection, an optimisation of the feature set using recursive feature elimination, and finally a gene-level sensitivity analysis for final selection of models. The predictive model based on 5 genes (MAPK8IP3 CRLF3, UNC13D, ILR9, and PRCKB) explains 14.9% of variance for KLH adaptive response. The models obtained for LTA and LPS use more genes and have lower predictive power, explaining respectively 7.8 and 4.5% of total variance. In comparison, the linear models built on genes identified by a standard statistical analysis explain 1.5, 0.5, and 0.3% of variance for KLH, LTA, and LPS response, respectively. The present study shows that machine learning methods applied to systems with a complex interaction network can discover phenotype-genotype associations with much higher sensitivity than traditional statistical models. It adds contribution to evidence suggesting a role of MAPK8IP3 in the adaptive immune response. It also indicates that CRLF3 is involved in this process as well. Both findings need additional verification.
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Affiliation(s)
- Aneta Polewko-Klim
- Institute of Computer Science, University of Bialystok, Białystok, Poland.
| | - Wojciech Lesiński
- Institute of Computer Science, University of Bialystok, Białystok, Poland
| | | | - Krzysztof Mnich
- Computational Centre, University of Bialystok, Białystok, Poland
| | - Maria Siwek
- Animal Biotechnology and Genetics Department, University of Technology and Life Sciences, Bydgoszcz, Poland
| | - Witold R Rudnicki
- Institute of Computer Science, University of Bialystok, Białystok, Poland; Computational Centre, University of Bialystok, Białystok, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
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Vermeersch E, Nuyttens BP, Tersteeg C, Broos K, De Meyer SF, Vanhoorelbeke K, Deckmyn H. Functional Genomics for the Identification of Modulators of Platelet-Dependent Thrombus Formation. TH OPEN 2019; 2:e272-e279. [PMID: 31249951 PMCID: PMC6524883 DOI: 10.1055/s-0038-1670630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/06/2018] [Indexed: 11/17/2022] Open
Abstract
Despite the absence of the genome in platelets, transcription profiling provides important insights into platelet function and can help clarify abnormalities in platelet disorders. The Bloodomics Consortium performed whole-genome expression analysis comparing in vitro–differentiated megakaryocytes (MKs) with in vitro–differentiated erythroblasts and different blood cell types. This allowed the identification of genes with upregulated expression in MKs compared with all other cell lineages, among the receptors BAMBI, LRRC32, ESAM, and DCBLD2. In a later correlative analysis of genome-wide platelet RNA expression with interindividual human platelet reactivity, LLRFIP and COMMD7 were additionally identified. A functional genomics approach using morpholino-based silencing in zebrafish identified various roles for all of these selected genes in thrombus formation. In this review, we summarize the role of the six identified genes in zebrafish and discuss how they correlate with subsequently performed mouse experiments.
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Affiliation(s)
- Elien Vermeersch
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak, Kortrijk, Belgium
| | | | - Claudia Tersteeg
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak, Kortrijk, Belgium
| | - Katleen Broos
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak, Kortrijk, Belgium
| | - Simon F De Meyer
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak, Kortrijk, Belgium
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak, Kortrijk, Belgium
| | - Hans Deckmyn
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak, Kortrijk, Belgium
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